[1] "Preparing Project:"
[1] "Hereeeeee"
[1] "Creating Object from..."
[1] "Patient data:"
[1] FALSE
[1] "Reading expression:tcga_coad_cms3.rds"
class: RangedSummarizedExperiment 
dim: 63856 66 
metadata(8): time_created recount3_version ... annotation recount3_url
assays(1): raw_counts
rownames(63856): ENSG00000278704.1 ENSG00000277400.1 ...
  ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y
rowData names(10): source type ... havana_gene tag
colnames(66): 2ebc7be8-627b-4767-a4fe-14e933e40c1c
  de456bd7-ef38-45fa-9e83-2ec44de69147 ...
  c739bc3e-2167-4ce0-988a-d1cf43669eeb
  3da25ae4-c004-4ee7-985e-6e880fcfedf2
colData names(937): rail_id external_id ... recount_seq_qc.errq
  BigWigURL
[1] "Map Barcodes..."
[1] "Normalize with CPM..."
[1] "LOG: There are 66 intial columns "
[1] "2ebc7be8-627b-4767-a4fe-14e933e40c1c"
[2] "de456bd7-ef38-45fa-9e83-2ec44de69147"
[3] "70b014fd-a0d0-418c-b55f-d09bae213d52"
[4] "c52a4bfa-e589-4974-91c3-5bcd1eecb970"
[5] "a2134c8c-b329-4536-b05f-70ef8e176349"
 [1] "TCGA-D5-6920-01A-11R-1928-07" "TCGA-D5-6530-01A-11R-1723-07"
 [3] "TCGA-AY-A54L-01A-11R-A28H-07" "TCGA-AZ-4313-01A-01R-1410-07"
 [5] "TCGA-AA-3560-01A-01R-0821-07" "TCGA-AA-A01V-01A-23R-A083-07"
 [7] "TCGA-CK-4952-01A-01R-1723-07" "TCGA-AA-A029-01A-01R-A00A-07"
 [9] "TCGA-D5-6538-01A-11R-1723-07" "TCGA-AA-3680-01A-01R-0905-07"
[11] "TCGA-AA-A00U-01A-01R-A002-07" "TCGA-AA-3556-01A-01R-0821-07"
[13] "TCGA-F4-6806-01A-11R-1839-07" "TCGA-G4-6323-01A-11R-1723-07"
[15] "TCGA-AA-3522-01A-01R-0821-07" "TCGA-DM-A288-01A-11R-A16W-07"
[17] "TCGA-AA-3713-01A-21R-1723-07" "TCGA-CK-4950-01A-01R-1723-07"
[19] "TCGA-DM-A28M-01A-12R-A16W-07" "TCGA-AA-3861-01A-01R-1022-07"
[21] "TCGA-DM-A28G-01A-11R-A16W-07" "TCGA-AA-3663-01A-01R-1723-07"
[23] "TCGA-G4-6304-01A-11R-1928-07" "TCGA-F4-6856-01A-11R-1928-07"
[25] "TCGA-CA-5796-01A-01R-1653-07" "TCGA-AA-3818-01A-01R-0905-07"
[27] "TCGA-AZ-5407-01A-01R-1723-07" "TCGA-AY-6386-01A-21R-1723-07"
[29] "TCGA-DM-A1D9-01A-11R-A155-07" "TCGA-AA-A00K-01A-02R-A002-07"
[31] "TCGA-DM-A1D6-01A-21R-A155-07" "TCGA-G4-6320-01A-11R-1723-07"
[33] "TCGA-CK-6747-01A-11R-1839-07" "TCGA-CA-5255-01A-11R-1839-07"
[35] "TCGA-AZ-6599-11A-01R-1774-07" "TCGA-AZ-6606-01A-11R-1839-07"
[37] "TCGA-AA-3522-11A-01R-A32Z-07" "TCGA-AA-A01Q-01A-01R-A002-07"
[39] "TCGA-AA-3854-01A-01R-0905-07" "TCGA-QG-A5YX-01A-11R-A28H-07"
[41] "TCGA-A6-6141-01A-11R-1774-07" "TCGA-G4-6322-01A-11R-1723-07"
[43] "TCGA-QG-A5Z2-01A-11R-A28H-07" "TCGA-G4-6293-01A-11R-1723-07"
[45] "TCGA-DM-A1D4-01A-21R-A155-07" "TCGA-AA-3655-11A-01R-1723-07"
[47] "TCGA-AA-3851-01A-01R-1022-07" "TCGA-AZ-6599-01A-11R-1774-07"
[49] "TCGA-AZ-4313-01A-01R-1410-07" "TCGA-AA-A02O-01A-21R-A16W-07"
[51] "TCGA-G4-6309-01A-21R-1839-07" "TCGA-CM-6172-01A-11R-1653-07"
[53] "TCGA-G4-6315-01A-11R-1723-07" "TCGA-AA-3713-11A-01R-1723-07"
[55] "TCGA-AA-3502-01A-01R-1410-07" "TCGA-AA-3681-01A-01R-0905-07"
[57] "TCGA-DM-A280-01A-12R-A16W-07" "TCGA-DM-A0X9-01A-11R-A155-07"
[59] "TCGA-CM-4746-01A-01R-1410-07" "TCGA-AA-A024-01A-02R-A00A-07"
[61] "TCGA-AA-3502-01A-01R-1410-07" "TCGA-AA-3655-01A-02R-1723-07"
[63] "TCGA-DM-A1DA-01A-11R-A155-07" "TCGA-AA-3663-11A-01R-1723-07"
[65] "TCGA-AD-6889-01A-11R-1928-07" "TCGA-D5-6539-01A-11R-1723-07"
[1] "LOG: There are  mapped columns  "
[1] "LOG: There are 64 non duplicate samples "
[1] "Batch correction for  tcga.gdc_platform"
[1] "LOG: There are 19833 genes that pass mintpm filtering "
[1] "Using logcpm..."
[1] "WARNING: no purity for "
[1] "LOG: There are 64 samples that pass purity filtering "
[1] "Tissue type:  tumor  "
[1] "Get final data..."
[1] "Saving table..."
[1] "LOG: Table dimensions: 19833 x 59 "
[1] "DONE!"
[1] "Saving RDS..."
